Prioritising candidate genes causing QTL using hierarchical orthologous groups.

Détails

Ressource 1Télécharger: bty615.pdf (978.32 [Ko])
Etat: Public
Version: Final published version
Licence: Non spécifiée
ID Serval
serval:BIB_6DAC1269D35C
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
Prioritising candidate genes causing QTL using hierarchical orthologous groups.
Périodique
Bioinformatics
Auteur(s)
Warwick Vesztrocy A., Dessimoz C., Redestig H.
ISSN
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
01/09/2018
Peer-reviewed
Oui
Volume
34
Numéro
17
Pages
i612-i619
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
A key goal in plant biotechnology applications is the identification of genes associated to particular phenotypic traits (for example: yield, fruit size, root length). Quantitative Trait Loci (QTL) studies identify genomic regions associated with a trait of interest. However, to infer potential causal genes in these regions, each of which can contain hundreds of genes, these data are usually intersected with prior functional knowledge of the genes. This process is however laborious, particularly if the experiment is performed in a non-model species, and the statistical significance of the inferred candidates is typically unknown.
This paper introduces QTLSearch, a method and software tool to search for candidate causal genes in QTL studies by combining Gene Ontology annotations across many species, leveraging hierarchical orthologous groups. The usefulness of this approach is demonstrated by re-analysing two metabolic QTL studies: one in Arabidopsis thaliana, the other in Oryza sativa subsp. indica. Even after controlling for statistical significance, QTLSearch inferred potential causal genes for more QTL than BLAST-based functional propagation against UniProtKB/Swiss-Prot, and for more QTL than in the original studies.
QTLSearch is distributed under the LGPLv3 license. It is available to install from the Python Package Index (as qtlsearch), with the source available from https://bitbucket.org/alex-warwickvesztrocy/qtlsearch.
Supplementary data are available at Bioinformatics online.
Mots-clé
Arabidopsis/genetics, Genomics, Molecular Sequence Annotation, Oryza/genetics, Quantitative Trait Loci, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
03/10/2018 11:40
Dernière modification de la notice
28/09/2019 5:08
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